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OPENSEQ.org
YDCI - Uncharacterized HTH-type transcriptional regulator YdcI
UniProt: P77171 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13752
Length: 307 (295)
Sequences: 36413
Seq/Len: 123.43
YDCI
Paralog alert: 0.88 [within 20: 0.50] - ratio of genomes with paralogs
Cluster includes: AAER ABGR ALLS CBL CYNR CYSB DMLR DSDC GCVA HCAR HDFR ICIA ILVY LEUO LRHA LYSR METR NAC NHAR OXYR PERR TDCA TTDR XAPR YAFC YAHB YBDO YBEF YBHD YCAN YCJZ YDCI YDHB YEEY YEIE YFER YFIE YGFI YHAJ YHJC YIAU YIDZ YJIE YNEJ YNFL
GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
80_R 84_A 3.755 1.00
25_Q 34_T 3.397 1.00
170_E 302_R 2.562 1.00
243_T 250_W 2.481 1.00
30_R 33_E 2.383 1.00
106_G 151_I 2.366 1.00
77_H 91_S 2.347 1.00
176_S 254_S 2.283 1.00
21_A 34_T 2.258 1.00
193_T 196_R 2.208 1.00
185_H 200_W 2.18 1.00
24_Q 79_V 2.176 1.00
104_R 133_Q 2.167 1.00
102_V 133_Q 2.167 1.00
102_V 131_T 2.164 1.00
171_L 174_L 2.144 1.00
81_V 85_I 2.1 1.00
77_H 84_A 2.061 1.00
122_Q 304_S 2.051 1.00
23_A 67_L 2.032 1.00
20_V 75_L 1.995 1.00
174_L 279_P 1.994 1.00
18_T 45_T 1.985 1.00
240_R 260_D 1.977 1.00
55_A 70_P 1.954 1.00
75_L 79_V 1.949 1.00
21_A 25_Q 1.92 1.00
20_V 79_V 1.909 1.00
20_V 24_Q 1.899 1.00
28_L 46_L 1.868 1.00
122_Q 300_A 1.868 1.00
21_A 24_Q 1.853 1.00
171_L 279_P 1.841 1.00
59_E 66_Q 1.832 1.00
244_V 260_D 1.827 1.00
18_T 42_L 1.81 1.00
244_V 265_T 1.79 1.00
178_K 254_S 1.786 1.00
74_F 88_A 1.777 1.00
203_V 248_Y 1.747 1.00
123_F 130_T 1.744 1.00
23_A 75_L 1.731 1.00
142_I 154_G 1.715 1.00
201_P 230_C 1.69 1.00
144_A 148_T 1.69 1.00
181_V 269_L 1.68 1.00
73_Q 91_S 1.674 1.00
20_V 78_A 1.672 1.00
69_L 72_E 1.652 1.00
29_G 39_Q 1.627 1.00
19_F 75_L 1.627 1.00
24_Q 34_T 1.618 1.00
25_Q 30_R 1.61 1.00
178_K 268_A 1.6 1.00
18_T 37_L 1.599 1.00
98_L 129_E 1.599 1.00
27_T 30_R 1.592 1.00
38_S 41_A 1.575 1.00
123_F 297_M 1.555 1.00
145_G 150_E 1.549 1.00
174_L 277_G 1.541 1.00
20_V 82_L 1.527 1.00
77_H 87_T 1.5 1.00
21_A 35_L 1.5 1.00
169_Y 281_G 1.496 1.00
15_H 45_T 1.448 1.00
56_R 59_E 1.443 1.00
81_V 88_A 1.431 1.00
113_L 237_S 1.422 1.00
212_R 216_D 1.414 1.00
153_I 294_C 1.411 1.00
122_Q 126_Q 1.405 0.99
15_H 52_L 1.404 0.99
72_E 76_T 1.4 0.99
15_H 48_E 1.395 0.99
100_N 129_E 1.381 0.99
74_F 89_G 1.375 0.99
13_L 85_I 1.368 0.99
203_V 239_S 1.367 0.99
258_K 262_R 1.365 0.99
77_H 80_R 1.343 0.99
12_R 15_H 1.333 0.99
121_G 125_Q 1.332 0.99
200_W 249_V 1.326 0.99
122_Q 125_Q 1.324 0.99
296_L 299_N 1.309 0.99
181_V 249_V 1.301 0.99
282_I 298_I 1.301 0.99
47_N 51_Q 1.292 0.99
137_M 141_M 1.284 0.99
290_F 294_C 1.283 0.99
146_L 154_G 1.278 0.99
168_N 284_T 1.27 0.99
260_D 265_T 1.269 0.99
168_N 286_V 1.265 0.99
145_G 151_I 1.261 0.99
124_H 201_P 1.237 0.98
233_T 239_S 1.235 0.98
104_R 135_A 1.233 0.98
19_F 23_A 1.228 0.98
52_L 89_G 1.227 0.98
298_I 302_R 1.226 0.98
186_P 200_W 1.225 0.98
241_Q 244_V 1.221 0.98
239_S 250_W 1.214 0.98
76_T 80_R 1.214 0.98
44_K 47_N 1.209 0.98
61_G 66_Q 1.207 0.98
77_H 88_A 1.204 0.98
84_A 87_T 1.2 0.98
37_L 41_A 1.199 0.98
112_A 136_T 1.198 0.98
73_Q 76_T 1.181 0.98
170_E 284_T 1.18 0.98
126_Q 300_A 1.176 0.98
43_S 47_N 1.166 0.97
124_H 230_C 1.155 0.97
22_V 46_L 1.155 0.97
19_F 58_F 1.152 0.97
28_L 65_A 1.15 0.97
123_F 300_A 1.149 0.97
147_K 166_G 1.146 0.97
23_A 58_F 1.142 0.97
254_S 258_K 1.14 0.97
153_I 282_I 1.139 0.97
17_H 86_N 1.138 0.97
190_E 196_R 1.136 0.97
192_V 196_R 1.133 0.97
259_D 263_H 1.132 0.97
183_P 265_T 1.127 0.97
19_F 57_L 1.124 0.97
175_E 255_G 1.124 0.97
67_L 71_G 1.123 0.97
241_Q 245_E 1.122 0.97
21_A 31_A 1.121 0.97
22_V 31_A 1.115 0.96
268_A 271_V 1.113 0.96
254_S 268_A 1.113 0.96
14_R 17_H 1.11 0.96
45_T 48_E 1.099 0.96
299_N 302_R 1.094 0.96
103_V 297_M 1.093 0.96
295_Q 299_N 1.088 0.96
181_V 185_H 1.088 0.96
16_L 78_A 1.086 0.96
180_V 257_V 1.086 0.96
183_P 267_V 1.086 0.96
73_Q 77_H 1.085 0.96
284_T 298_I 1.081 0.95
240_R 244_V 1.078 0.95
182_R 246_Y 1.077 0.95
121_G 245_E 1.073 0.95
44_K 48_E 1.065 0.95
179_L 249_V 1.062 0.95
37_L 42_L 1.061 0.95
185_H 201_P 1.059 0.95
80_R 87_T 1.058 0.95
123_F 127_Q 1.054 0.95
219_V 224_C 1.05 0.94
81_V 84_A 1.038 0.94
169_Y 283_L 1.035 0.94
171_L 281_G 1.034 0.94
156_G 283_L 1.033 0.94
187_L 190_E 1.033 0.94
126_Q 303_K 1.03 0.94
127_Q 296_L 1.024 0.93
233_T 242_L 1.012 0.93
58_F 65_A 1.006 0.93
133_Q 232_E 1.002 0.92
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
2esnA40.98051000.131Contact Map0.753
1uthA10.99021000.134Contact Map0.73
3fxqA20.96741000.141Contact Map0.774
1al3A10.95771000.148Contact Map0.767
3fzvA40.96421000.148Contact Map0.709
1ixcA20.94791000.15Contact Map0.759
2h98A20.94461000.15Contact Map0.753
2h9bA20.94461000.16Contact Map0.742
3szpA20.94461000.175Contact Map0.77
3hhgA80.95111000.177Contact Map0.925
Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.
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